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java.lang.StringIndexOutOfBoundsException Error while reading Binary String

I have a long String with binary values. And i have a hash map that has the Binary digits as a key and char as a value. I have a function that supposed to read the binary string using 2 pointers and compare with hashmap and store the corresponding char in main.decodedTxt. However, im getting string out of bound exception for this. I don't know how to solve this. I'm getting exception on "String temp =" line. I have a picture link of the console output to see better picture.
public static void bitStringToText (String binText){
String bs = binText;
int from =0;
int to = 1;
while(bs != null){
String temp = bs.substring(from, to);
if (main.newMapDecoding.containsKey(temp)){
main.decodedTxt += main.newMapDecoding.get(temp);
from =to;
to = from +1;
} else {
to = to + 1;
}
}
}
Image of console exception is here

First of all there is no need to check if bs is null because no part of your code changes the value of bs. Your current code will cross the possible index of your binText at some point. It's better to loop just binText and check if you find something within it. After all you have to traverse the complete string anyways. Change your code as follows
public static void bitStringToText (String binText){
//no need to do this if you are not modifying the contents of binText
//String bs = binText;
int from =0;
int to = 1;
int size = binText.length();
String temp = "";
while(to <= size ){
temp = binText.substring(from, to);
if (main.newMapDecoding.containsKey(temp)){
main.decodedTxt += main.newMapDecoding.get(temp);
from =to;
to = from +1;
} else {
to = to + 1;
}
}
}
Hope it helps.

First, give it a try to practice debugging. It is an easy case. Either use run in debug mode (place break point on String temp = bs.substring(from, to); line) or print values of from and to before the same line. It will help to understand what is going on.
Solution:
If bs is not null you will always have StringIndexOutOfBoundsException. Because you are not checking if to is pointing to not existed index of bs String. Easiest example of the first one will be empty String: bs == "".
One of the solution could be to replace condition in while to while (to <= bs.length()).

Detecting duplicates in a file generated using the sliding window concept

I am working on a project where I have to parse a text file and divide the strings into substrings of a length that the user specifies. Then I need to detect the duplicates in the results.
So the original file would look like this:
ORIGIN
1 gatccaccca tctcggtctc ccaaagtgct aggattgcag gcctgagcca ccgcgcccag
61 ctgccttgtg cttttaatcc cagcactttc agaggccaag gcaggcgatc agctgaggtc
121 aggagttcaa gaccagcctg gccaacatgg tgaaacccca tctctaatac aaatacaaaa
181 aaaaaacaaa aaacgttagc caggaatgag gcccggtgct tgtaatccta aggaaggaga
241 ccaccactcc tcctgctgcc cttcccttcc ccacaccgct tccttagttt ataaaacagg
301 gaaaaaggga gaaagcaaaa agcttaaaaa aaaaaaaaaa cagaagtaag ataaatagct
I loop over the file and generate a line of the strings then use line.toCharArray() to slide over the resulting line and divide according to the user specification. So if the substrings are of length 4 the result would look like this:
GATC
ATCC
TCCA
CCAC
CACC
ACCC
CCCA
CCAT
CATC
ATCT
TCTC
CTCG
TCGG
CGGT
GGTC
GTCT
TCTC
CTCC
TCCC
CCCA
CCAA
Here is my code for splitting:
try {
scanner = new Scanner(toSplit);
while (scanner.hasNextLine()) {
String line = scanner.nextLine();
char[] chars = line.toCharArray();
for (int i = 0; i < chars.length - (k - 1); i++) {
String s = "";
for(int j = i; j < i + k; j++) {
s += chars[j];
}
if (!s.contains("N")) {
System.out.println(s);
}
}
}
}
My question is: given that the input file can be huge, how can I detect duplicates in the results?

If You want to check duplicates a Set would be a good choice to hold and test data. Please tell in which context You want to detect the duplicates: words, lines or "output chars".

You can use a bloom filter or a table of hashes to detect possible duplicates and then make a second pass over the file to check if those "duplicate candidates" are true duplicates or not.
Example with hash tables:
// First we make a list of candidates so we count the times a hash is seen
int hashSpace = 65536;
int[] substringHashes = new int[hashSpace];
for (String s: tokens) {
substringHashes[s.hashCode % hashSpace]++; // inc
}
// Then we look for words that have a hash that seems to be repeated and actually see if they are repeated. We use a set but only of candidates so we save a lot of memory
Set<String> set = new HashSet<String>();
for (String s: tokens) {
if (substringHashes[s.hashCode % hashSpace] > 1) {
boolean repeated = !set.add(s);
if (repeated) {
// TODO whatever
}
}
}

You could do something like this:
Map<String, Integer> substringMap = new HashMap<>();
int index = 0;
Set<String> duplicates = new HashSet<>();
For each substring you pull out of the file, add it to substringMap only if it's not a duplicate (or if it is a duplicate, add it to duplicates):
if (substringMap.putIfAbsent(substring, index) == null) {
++index;
} else {
duplicates.add(substring);
}
You can then pull out all the substrings with ease:
String[] substringArray = new String[substringMap.size()];
for (Map.Entry<String, Integer> substringEntry : substringMap.entrySet()) {
substringArray[substringEntry.getValue()] = substringEntry.getKey();
}
And voila! An array of output in the original order with no duplicates, plus a set of all the substrings that were duplicates, with very nice performance.

Get Portion of String

I need to get the values after "Swap:".
I've already developed a method to get the output from a shell command so I have a string that contains everything you see in the picture but now from the string I want to get ONLY the value after the Swap: How can i do this? These value are variable and can be even all three 0.

Let's say you have the text stored in a String called textContent. Assuming the Swap-line is the last part of your String, then you could do something like this:
int index = textContent.indexOf("Swap:");
index += "Swap:".length();
textContent.subString(index);

Try this:
String[] stringParts = text.substring(text.indexOf("Swap:") + 5).trim().split("( )+");
int[] parts = new int[stringParts.length];
for (int i = 0; i < stringParts.length; i++)
parts[i] = Integer.parseInt(stringParts[i]);
It will fill an integer array will the values after the "Swap" part.

Since you have already stored the output of the shell command, you simply need to do some string manipulation to search and extract the relevant information. The following particular string manipulation methods might be of interest to you: trim(), indexOf(), and substring().
Below is a simple example code on how to extract the value under the total's column using the above String methods:
public class ShellOutput {
public ShellOutput() {
final String extract = "Swap:"; // the keyword to search
String shellOutput = "Swap: 75692 29657 0"; // your shell output
int position = shellOutput.indexOf(extract); // get the position of the Swap: text
if (position != -1) {
String swapLine = shellOutput.substring(position + extract.length()); // remove everything except the swap line
String numbers = swapLine.trim(); // assuming they are spaces, otherwise do some operations to remove tabs if used
int firstSpace = numbers.indexOf(' '); // get the first space or change to a tab character if it is used
String totalNumber = numbers.substring(0, firstSpace); // remove up to the first found after the number
System.out.println("Total = " + totalNumber);
} else {
System.out.println("No '" + extract + "' segment found.");
}
}
public static void main(String[] args) {
new ShellOutput();
}
}
Output: Total = 75692

Code optimization by chosing another datastructure

I have a piece of code that needs to be optimized.
for (int i = 0; i < wordLength; i++) {
for (int c = 0; c < alphabetLength; c++) {
if (alphabet[c] != x.word.charAt(i)) {
String res = WordList.Contains(x.word.substring(0,i) +
alphabet[c] +
x.word.substring(i+1));
if (res != null && WordList.MarkAsUsedIfUnused(res)) {
WordRec wr = new WordRec(res, x);
if (IsGoal(res)) return wr;
q.Put(wr);
}
}
}
Words are represented by string. The problem is that the code on line 4-6 creates to many string objects, because strings are immutable.
Which data structure should I change my word representation to, if I want to get faster code ? I have tried to change it to char[], but then I have problem with getting the following code work:
x.word.substring(0,i)
How to get subarray from a char[] ? And how to concatenate the char and char[] on line 4.6 ?
Is there any other suitable and mutable datastrucure that I can use ? I have thought of stringbuffer but can't find suitable operations on stringbuffers.
This function generates, given a specific word, all the word that differs by one character.
WordRec is just a class with a string representing a word, and a pointer to the "father" of that word.
Thanks in advance

You can reduce number of objects by using this approach:
StringBuilder tmp = new StringBuilder(wordLength);
tmp.append(x.word);
for (int i=...) {
for (int c=...) {
if (...) {
char old = tmp.charAt(i);
tmp.setCharAt(i, alphabet[c]);
String res = tmp.toString();
tmp.setCharAt(i, old);
...
}
}
}

Java loop not creating string correctly

I'm using a for loop to append an "m" on to a string array, then passing each string to a DDE connection to download a stock quote.
String[] symbols = {"AUDUSD", "EURUSD", "GBPUSD", "USDJPY"};
String ibfxSym[] = new String[symbols.length];
for(int i = 0; i<symbols.length;i++) {
ibfxSym[i] = symbols[i] + "m";
}
// start DDE
for (int i = 0; i < connections.length; i++) {
try {
connections[i].getQuote(ibfxSym[i]);
} catch (Exception e) {
System.out.println("error");
}
That does not work, but if I pass in:
String[] ibfxSym = {"AUDUSDm", "EURUSDm", "GBPUSDm", "USDJPYm"};
instead of the loop it works just fine. I've tried printing each string as it is created in the loop, and they look the same. Is there some weird formatting the loop is adding that I can't see? I even tried:
ibfxSym[i] = String.valueOf(ibfxSym[i].trim());
to see if there was maybe a carriage return or something being appended that I couldn't see. Any ideas about what's going wrong here?
Thanks.

You're not reading from the same array that you're modifying...
ibfxSym[i] = symbols[i] + "m";
for (int i = 0; i < connections.length; i++) {
try {
connections[i].getQuote(ibfxSym[i]);
In other words, you are assuming that i, being derived from iterating over connections, is also a valid index for ibfxSym.

Your loop is working just fine, the connection loop instead would work only if your connections array maps your ibfxSym array though..

if
connections.length
is bigger than
ibfxSym.length
or in this case 4, you should get an array index out of bounds exception i think.

Have you tried to do this:
for(int i = 0; i<symbols.length;i++) {
ibfxSym[i] = new String(symbols[i] + "m");
}